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- PDB-1mup: PHEROMONE BINDING TO TWO RODENT URINARY PROTEINS REVEALED BY X-RA... -

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Basic information

Entry
Database: PDB / ID: 1mup
TitlePHEROMONE BINDING TO TWO RODENT URINARY PROTEINS REVEALED BY X-RAY CRYSTALLOGRAPHY
ComponentsMAJOR URINARY PROTEIN
KeywordsPHEROMONE-BINDING
Function / homology
Function and homology information


pheromone binding / positive regulation of lipid metabolic process / negative regulation of lipid biosynthetic process / positive regulation of glucose metabolic process / odorant binding / energy reserve metabolic process / insulin receptor activity / negative regulation of insulin secretion involved in cellular response to glucose stimulus / cellular response to lipid / heat generation ...pheromone binding / positive regulation of lipid metabolic process / negative regulation of lipid biosynthetic process / positive regulation of glucose metabolic process / odorant binding / energy reserve metabolic process / insulin receptor activity / negative regulation of insulin secretion involved in cellular response to glucose stimulus / cellular response to lipid / heat generation / small molecule binding / locomotor rhythm / negative regulation of lipid storage / negative regulation of gluconeogenesis / aerobic respiration / mitochondrion organization / glucose homeostasis / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of DNA-templated transcription / positive regulation of gene expression / extracellular space / nucleus / cytosol
Similarity search - Function
Major urinary protein / Lipocalin / Lipocalin family conserved site / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Lipocalin signature. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
: / 2-(SEC-BUTYL)THIAZOLE / Major urinary protein 6
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsBocskei, Z. / Flower, D.R. / Groom, C.R. / Phillips, S.E.V. / North, A.C.T.
Citation
Journal: Nature / Year: 1992
Title: Pheromone binding to two rodent urinary proteins revealed by X-ray crystallography.
Authors: Bocskei, Z. / Groom, C.R. / Flower, D.R. / Wright, C.E. / Phillips, S.E. / Cavaggioni, A. / Findlay, J.B. / North, A.C.
#1: Journal: Experientia / Year: 1992
Title: Pheromone Binding Proteins of the Mouse (Mus Musculus)
Authors: Bacchini, A. / Gaetani, E. / Cavaggioni, A.
#2: Journal: J.Mol.Biol. / Year: 1991
Title: Crystallization of and Preliminary X-Ray Data for the Mouse Major Urinary Protein and Rat Alpha-2U Globulin
Authors: Bocskei, Z. / Findlay, J.B.C. / North, A.C.T. / Phillips, S.E.V. / Somers, W.S. / Wright, C.E. / Lionetti, C. / Tirindelli, R. / Cavaggioni, A.
History
DepositionSep 21, 1992Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Jul 17, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.5Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.6Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MAJOR URINARY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7216
Polymers19,1301
Non-polymers5915
Water1,38777
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.300, 57.300, 110.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein MAJOR URINARY PROTEIN


Mass: 19130.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / References: UniProt: P02762
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-TZL / 2-(SEC-BUTYL)THIAZOLE


Mass: 141.234 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H11NS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsTHE ENTRY INCLUDES FOUR CADMIUM IONS WITH VARYING OCCUPANCIES.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.87 %
Crystal grow
*PLUS
pH: 5.5 / Method: vapor diffusion, hanging drop
Details: taken from Bocskei, Z. et al (1991). J. Mol. Biol., 218, 699-701.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
112 mg/mlprotein1drop
230 mMmaleate1drop
440-70 mM1reservoirCdCl2
5200 mMmaleate1reservoir
31drop0.005ml of well solution

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.4→14 Å / Rfactor Rwork: 0.191 / Rfactor obs: 0.191
Refinement stepCycle: LAST / Resolution: 2.4→14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1242 0 13 77 1332
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.026
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it9.295
X-RAY DIFFRACTIONx_mcangle_it10.925
X-RAY DIFFRACTIONx_scbond_it8.073
X-RAY DIFFRACTIONx_scangle_it11.665
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 14 Å / Rfactor obs: 0.191
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONt_bond_d0.02
X-RAY DIFFRACTIONt_angle_d0.040.08
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_improper_angle_d
X-RAY DIFFRACTIONt_planar_d0.050.081
X-RAY DIFFRACTIONt_plane_restr0.020.071
X-RAY DIFFRACTIONt_chiral_restr0.150.224
X-RAY DIFFRACTIONt_mcbond_it
X-RAY DIFFRACTIONt_scbond_it
X-RAY DIFFRACTIONt_mcangle_it
X-RAY DIFFRACTIONt_scangle_it

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